So the whole problem has arisen because Paddington is listed somewhere as a legitimate London terminal for journeys from Aylesbury, but the shortest route for that journey is now via Oxford? Have I got it right?
No, the problem has arisen because the routing guide has become so complicated that only one person (a well-respected forum member) understands it.
Either there are some public trains (as opposed to the Central Line) South Ruislip <> Greenford, or there aren't. If there are, then Princes Risborough to Paddington should remain valid on a London Terminals ticket, with Greenford as the only valid route. That should not require any squeezement.
If there aren't, and won't be in the foreseeable future, then Paddington should be delisted for this flow.
There is, I think, a wider issue. A ticket from Aylesbury (and other places, actually) to Paddington routed via Oxford, issued at the same price as a ticket to Marylebone, has plainly been issued by mistake. I don't know how many such tickets have been sold. But I think that all, or almost all, purchasers of such a ticket would know that it was a mistake. The law on contracts entered into by mistake is complicated, but they can be void. There is an entertaining leading case when a salvage tug turned out to be lots further away from a stricken vessel than the parties believed; the Court of Appeal upheld the contract, because the tug could have got where it was wanted, just a lot later than expected.